You are right, that would make sense! Have a good weekend, Pierre Pierre Bourguet Postdoc Gregor Mendel Institute of Molecular Plant Biology GmbH Dr. Bohr-Gasse 3, 1030 Vienna, Austria pierre.bourguet@gmi.oeaw.ac.at http://www.gmi.oeaw.ac.at [cid:gmi_48f983b7-0679-4d21-99bc-bda376e5bf6b.png] ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: 06 September 2024 17:54 To: Bourguet,Pierre <pierre.bourguet@gmi.oeaw.ac.at> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] error in the documentation? Hi Pierre, Thanks for letting us know! Hmmm, now I wonder if it is really supposed to say "lower in PAE" but I will doublecheck and it will be fixed soon. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 6, 2024, at 4:55 AM, Bourguet,Pierre via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX support,
First of all, thank you for developing & maintaining such an easy-to-use software. I am not trained as a structural biologist, but I looking at more and more structures thanks to alphafold. The journey is much nicer since I switched to ChimeraX!
I have noticed the following inconsistency in the documentation. https://rbvi.ucsf.edu/chimerax/docs/user/commands/alphafold.html#contacts
"If one set of entities is higher-confidence (lower in pLDDT) than the other, it is usually best to specify them as the aligned set so that the coloring will show the error values of the lower-confidence set."
My understanding is that it should say "(higher in pLDDT)".
Hopefully that helps!
Best, Pierre Pierre Bourguet Postdoc
Gregor Mendel Institute of Molecular Plant Biology GmbH Dr. Bohr-Gasse 3, 1030 Vienna, Austria pierre.bourguet@gmi.oeaw.ac.at http://www.gmi.oeaw.ac.at
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